Comments (5)
Alanocallaghan
commented on August 11, 2024
1
No bother, I might add a seealso to some of the docs (partly to remind myself)
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antagomir
commented on August 11, 2024
Here an example using TreeSummarizedExperiment objects (which inherit SCE):
# Load libraries
library(mia)
library(scater)
# Load demo data
data(hitchip1006, package="miaTime")
tse <- hitchip1006
# Run MDS to get reducedDim
tse <- runMDS(tse, exprs_values="counts")
# Plot reducedDim and retrieve ggplot object
p <- plotReducedDim(tse, dimred="MDS")
# Add trajectory between data points from the same subject
p + geom_path(aes(x=X, y=Y, group=subject),
data = data.frame(reducedDim(tse), colData(tse))
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antagomir
commented on August 11, 2024
I realized that the solution (last point) is so straighforward in practice that this does not necessarily require updates into plotReducedDim functionality.
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Alanocallaghan
commented on August 11, 2024
What about scuttle::makePerCellDF?
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antagomir
commented on August 11, 2024
Ah yes, perfect!
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Related Issues (20)
- Issue with runTSNE and deprecated parameter, i.e. use_dimred? HOT 1
- Centering labels in plotReducedDim with force = 0 HOT 3
- Pass to num_jobs for snifter
- `plotDots` should document that `features=` can accept a factor to control the order HOT 6
- Handling genes with zero expression when using `scale = TRUE` in `plotDots()` HOT 3
- Add a `projectReducedDims` function HOT 5
- Use import or importFrom for `pheatmap` HOT 3
- can plotUMAP offer a order parameter HOT 6
- Create rasters for plots involving many, many points HOT 4
- Option not to plot the points in violin plots HOT 5
- fill_by for violin plots HOT 5
- plotGroupedHeatmap not colouring appropriately. HOT 1
- ggbeeswarm dependency HOT 1
- aes_string deprecation leads to incredibly hacky code HOT 4
- plotPCA not coloring points HOT 2
- Adding alias to exprs_values argument HOT 3
- Argument naming: "assay_name" (scater) vs. "assay.type" (scuttle) HOT 2
- Use scattermore to speed up plotColData and plotReducedDim for large datasets HOT 4
- Gene names in nmf basis HOT 2
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